Install directions¶
This section covers the basics of how to download and install TIMBIR.
Dependencies¶
- MPI compiler (Intel or Open MPI)
- OpenMP
- make utility
Dependencies Install¶
Install MPI ( Here I use openMPI as a example):
$ wget https://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-1.10.2.tar.gz $ tar xvzf openmpi-1.10.2.tar.gz $ cd <openmpi path> $ ./configure --prefix=<your mpi install path> $ make all install
Install HDF5 library. First go to https://www.hdfgroup.org/HDF5/release/obtainsrc.html#conf to find the appropriate hdf5 library for your platform (here we use hdf5-1.8.16.tar as example:
$ tar xvf hdf5-1.8.16.tar $ cd <hdf5 path> $ ./configure --prefix=/clhome/KYUE/lib/hdf5 --enable-fortran --enable-cxx $ make $ make install
Set your library path with HDF5 library and MPI library (here we use bash as example):
$ vi env.sh (create a bash script) $ export HDF5_BASE=<hdf5 full path> $ export MPI_BASE=<MPI full path> $ export PATH = ${MPI_BASE}/bin:${HDF5_BASE}/bin:$PATH $ export LD_LIBRARY_PATH= = ${MPI_BASE}/lib:${HDF5_BASE}/lib64:$PATH $ source env.sh
Compiling TIMBIR¶
To compile the MBIR algorithm code:
$ git clone https://github.com/adityamnk/timbir.git timbir
$ cd timbir/src/MBIR_4D
This generates library files in timbir/src/lib. For more information, read the README in timbir/src/MBIR_4D.
Running the reconstruction algorithm¶
If the input data format is a standard binary, run the code in timbir/src/reconstruct/bin_data. For more information on data format and running the code, read the README in timbir/src/reconstruct/basic:
$ cd timbir/src/reconstruct/bin_data
$ make
This generates executables in the same folder.
If the input data is in HDF format used at APS, run the code in timbir/src/reconstruct/aps_data. For more information on data format and running the code, read the README in timbir/src/reconstruct/aps_data:
$ cd timbir/src/reconstruct/aps_data
$ make
This generates executables in the same folder.
If the input data is in standard HDF format, run the code in timbir/src/reconstruct/std_data. For more informantion on data format and running the code, read the README in timbir/src/reconstruct/std_data:
$ cd timbir/src/reconstruct/std_data
$ make #Generates executables in the same folder